I choose Richards over Santana simply because I'd rather listen to the Stones (and Zeppelin over Hendrix, GNR over JLH, and Floyd over SRV (AFAIK)). I realise we're judging the guitarists here and not the bands, but if the music that their greatness results in does nothing for me (and, admittedly, none of them at this stage does very much) then no amount of technical superiority or innovation or anything else matters.
My go-to guitarist when I think of the best around today is Frusciante, but then I think of the music he makes and I can't be doing with any of it, neither solo nor Peppers. The same could be said of the Peppers drummer's drumming and Flea's bassing (when he's not slapping like an arse).
But I don't feel that the opposite is true either; that a band made up of technically unremarkable musicians whose music I love is in any way indicative of individual greatness, so perhaps the resulting music doesn't matter after all.